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Comparative Analysis of Ralstonia solanacearum Methylomes

Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing t...

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Autores principales: Erill, Ivan, Puigvert, Marina, Legrand, Ludovic, Guarischi-Sousa, Rodrigo, Vandecasteele, Céline, Setubal, João C., Genin, Stephane, Guidot, Alice, Valls, Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390034/
https://www.ncbi.nlm.nih.gov/pubmed/28450872
http://dx.doi.org/10.3389/fpls.2017.00504
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author Erill, Ivan
Puigvert, Marina
Legrand, Ludovic
Guarischi-Sousa, Rodrigo
Vandecasteele, Céline
Setubal, João C.
Genin, Stephane
Guidot, Alice
Valls, Marc
author_facet Erill, Ivan
Puigvert, Marina
Legrand, Ludovic
Guarischi-Sousa, Rodrigo
Vandecasteele, Céline
Setubal, João C.
Genin, Stephane
Guidot, Alice
Valls, Marc
author_sort Erill, Ivan
collection PubMed
description Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants.
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spelling pubmed-53900342017-04-27 Comparative Analysis of Ralstonia solanacearum Methylomes Erill, Ivan Puigvert, Marina Legrand, Ludovic Guarischi-Sousa, Rodrigo Vandecasteele, Céline Setubal, João C. Genin, Stephane Guidot, Alice Valls, Marc Front Plant Sci Plant Science Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants. Frontiers Media S.A. 2017-04-13 /pmc/articles/PMC5390034/ /pubmed/28450872 http://dx.doi.org/10.3389/fpls.2017.00504 Text en Copyright © 2017 Erill, Puigvert, Legrand, Guarischi-Sousa, Vandecasteele, Setubal, Genin, Guidot and Valls. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Erill, Ivan
Puigvert, Marina
Legrand, Ludovic
Guarischi-Sousa, Rodrigo
Vandecasteele, Céline
Setubal, João C.
Genin, Stephane
Guidot, Alice
Valls, Marc
Comparative Analysis of Ralstonia solanacearum Methylomes
title Comparative Analysis of Ralstonia solanacearum Methylomes
title_full Comparative Analysis of Ralstonia solanacearum Methylomes
title_fullStr Comparative Analysis of Ralstonia solanacearum Methylomes
title_full_unstemmed Comparative Analysis of Ralstonia solanacearum Methylomes
title_short Comparative Analysis of Ralstonia solanacearum Methylomes
title_sort comparative analysis of ralstonia solanacearum methylomes
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5390034/
https://www.ncbi.nlm.nih.gov/pubmed/28450872
http://dx.doi.org/10.3389/fpls.2017.00504
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